A comparison between fatty acid methyl ester profiling methods (PLFA and EL-FAME) as soil health indicators

Fatty acid methyl ester (FAME) profiling for characterizing microbial community composition typically is conducted via phospholipid fatty acid (PLFA) or ester-linked fatty acid methyl ester (EL-FAME) methods. As soil health assessments aim to be utilized across the nation and globe, the robust measurement and interpretation of microbial communities across a range of soils and environments will be necessary. This study compared PLFA and EL-FAME methods for detecting and interpreting profiles of microbial community composition in croplands across a wide geographic area using a total of 172 soil samples from 14 states representing a wide range of soil properties. Overall, PLFA and EL-FAME provided comparable biomarkers in terms of microbial community composition. The Spearman's Rank correlation test showed positive correlations (r = 0.37-0.71) between PLFA and EL-FAME methods for absolute abundance of total FAME and individual microbial groups including fungi (saprophytic fungi [SF], arbuscular mycorrhizal fungi [AMF], and general fungi [F]) and all bacterial groups (Gram positive [GMP], Gram negative [GMN], and Actinobacteria). In both methods, a common set of fatty acids were influential in differentiating samples. The main differences in biomarker abundances between the two methods were that fungal and Actinobacteria biomarkers (e.g., 16:1 omega 5c [AMF], 18:1 omega 9c [F], 18:3 omega 6c [F], and 10Me16:0 [Actinobacteria]) were more abundant or critical in EL-FAME profiling (large variation among soil samples and sensitive to soil properties), but bacterial biomarkers such as i15:0 (GMP), 16:1 omega 7c (GMN), 18:1 omega 7c (GMN), and cy19:0 omega 7c (GMN) were more dominant and responsive to soil properties in PLFA profiling. The practical advantages of EL-FAME are lower cost and simpler methodology. Although both methods produced similar microbial profile abundances for important microbial markers, PLFA was more sensitive to the wide range of soil chemical properties in this sample set including pH, clay content, soil organic matter, and active carbon.